|
| Status |
Public on Jun 07, 2013 |
| Title |
T47D-overexpressing ELF5-input DNA-24hour |
| Sample type |
SRA |
| |
|
| Source name |
T47D cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: T47D
treatment: doxycycline
timepoint: 24h
enrichment: input DNA
|
| Treatment protocol |
Drug treatments were performed with Dox (Clontech) at 0.1 μg/ml, R5020 (Du Pont) at 10 nM or 17β-estradiol (Sigma) at 10 mM. Dox-containing medium was changed every 24 hours to ensure optimum Dox activity. Adherent cells on tissue culture plates were incubated in fresh, warm, serum-free medium supplemented with 1% formaldehyde, at 37°C for 10 minutes.
|
| Growth protocol |
Human breast carcinoma T47D-EcoR (Musgrove et al., 2001) cell lines were grown in RPMI 1640 medium (Invitrogen) supplemented with 10 % Tet System Approved fetal bovine serum (FBS) (Clontech). Cells infected with pHUSH-ProEX-based produced by the Platinum E cell line (Morita et al., 2000). Transient transfection with plasmid constructs used FuGENE reagent (Roche) or Lipofectamine LTX (Invitrogen) according to manufacturer’s instructions. Cells were maintained in the presence of puromycin (Sigma) at a concentration of 2μg/mL.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were washed 2 times with cold PBS and scraped into 600 μl PBS with protease inhibitors (P8340, Sigma). Fixed cells were spun for 2 minutes at 6,000xg, washed as before and snap frozen in liquid nitrogen.
ChIP-Seq as previously described (doi:10.1016/j.ymeth.2009.03.001) using a 50%–50% mixture of V5-specific antibody and the Santa Cruz N20 anti ELF5 antibody, or no antibody for the input files. DNA was processed for Illumina sequencing using 36-bp reads on a GAIIx.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
T47D cell lines, overexpressing ELF5 with V5 tag, input DNA, replicate 1
|
| Data processing |
Sequences were aligned against NCBI Build 36.3 of the human genome using MAQ (http://maq.sourceforge.net/) with default parameters.
The aligned reads were converted to BED format using a custom script.
Reads were filtered for uniquely mapped tags
Wiggle coverage files generated, normalised per million reads.
Genome_build: ncbi36.3
Supplementary_files_format_and_content: *.filter.bed.gz files contain the aligned reads, filtered for unique mappers only. These are standard BED6 formatted files (chr,start,stop,name=read_id,score=mapping_quality,strand)
Supplementary_files_format_and_content: *wig.gz files are standard wiggle files, at 20bp resolution, indicating read depth across the genome, normalised per 1e06 reads.
|
| |
|
| Submission date |
Jun 06, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Mark Cowley |
| E-mail(s) |
m.cowley@garvan.org.au
|
| Organization name |
Garvan Institute of Medical Research
|
| Department |
Genome Informatics & Clinical Genomics
|
| Lab |
Dinger lab
|
| Street address |
384 Victoria St.
|
| City |
Darlinghurst |
| State/province |
NSW |
| ZIP/Postal code |
2010 |
| Country |
Australia |
| |
|
| Platform ID |
GPL10999 |
| Series (2) |
| GSE30407 |
The ets transcription factor ELF5 suppresses the estrogen sensitive phenotype and contributes to antiestrogen resistance in luminal breast cancer. |
| GSE31216 |
The ets transcription factor ELF5 suppresses the estrogen sensitive phenotype and contributes to antiestrogen resistance in luminal breast cancer. [human ChIP-Seq] |
|
| Relations |
| BioSample |
SAMN02191890 |
| SRA |
SRX297110 |
